CFAP73 p.Asn257=
c.771C>T · rs149289099 · VCV2643351
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.915%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.091 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.7 | GERP 1.4, phastCons 0.92 |
| Overall | ||
| CADD | 11.53 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.915%
European (non-Finnish) · 10,496/1,146,780 alleles
Filtering AF
0.901%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.895%
Overall
0.721%
11,180/1,551,438 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.915% | 109 |
| Amishnot grpmax-eligible | 0.548% | 182 |
| Remaining individualsnot grpmax-eligible | 0.507% | 197 |
| Finnishnot grpmax-eligible | 0.402% | 249 |
| African / African-American | 0.104% | 963 |
| Admixed American | 0.0765% | 1,307 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0558% | 1,791 |
| Middle Eastern | 0.0167% | 5,990 |
| South Asian | 0.00119% | 84,034 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CFAP73
- Protein
- p.Asn257=
- Coding
- c.771C>T
- MANE Select
- NM_001144872
- dbSNP
- rs149289099
- Type
- single nucleotide variant
- Location
- chr12:113155340 (GRCh38)
- Gene constraint
- LOEUF 1.354 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.57 · 1 PDB
Similar variants
- DDX54 p.Gly875Asp Uncertain significance ★★ ⚠ same type
- CFAP73 p.Ala103Val Uncertain significance ★ ⚠ same type
- CFAP73 p.Ala109Gly Uncertain significance ★ ⚠ same type
- CFAP73 p.Ala150Glu Uncertain significance ★ ⚠ same type
- CFAP73 p.Ala171Thr Uncertain significance ★ ⚠ same type
- CFAP73 p.Ala175Val Uncertain significance ★ ⚠ same type
- CFAP73 p.Ala186Ser Uncertain significance ★ ⚠ same type
- CFAP73 p.Ala214Thr Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cfap73-p-asn257 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown